1988–89 Albanian Cup (Albanian: Kupa e Shqipërisë) was the thirty-seventh season of Albania's annual cup competition. It began on August 1988 with the First Round and ended on May 1989 with the Final match. The winners of the competition qualified for the 1989-90 first round of the UEFA Cup. KS Flamurtari were the defending champions, having won their second Albanian Cup last season. The cup was won by Dinamo Tirana.
The first round was played in a single round-robin matches within 4 qualifying groups. The other rounds were played in a two-legged format similar to those of European competitions. If the aggregated score was tied after both games, the team with the higher number of away goals advanced. If the number of away goals was equal in both games, the match was decided by extra time and a penalty shootout, if necessary.